Hutspot This is a multisample DNA variant calling pipeline for use in diagnostics based on Snakemake, bwa and the GATK HaplotypeCaller. Features Any number of samples is supported Whole-genome calling, regardless of wet-lab library preparation. Follows modern best practices Each sample is individually called as as a GVCF. A multisample VCF is then produced by genotyping the collection of GVCFs. Data parallelization for calling and genotyping steps. Using ~100 chunks, we call an entire exome in ~15 minutes! Reasonably fast. 96 exomes in < 24 hours. No unnecessary jobs Coverage metrics for any number of bed files. Fully containerized rules through singularity and biocontainers. Legacy conda environments are available as well. Optionally sub-sample inputs when number of bases exceeds a user-defined threshold